Characterization of carbapenemase-producing Enterobacteriaceae from colonized patients in a university hospital in Madrid, Spain, during the R-GNOSIS project depicts increased clonal diversity over time with maintenance of high-risk clones

Abstract

To describe the incidence and microbiological features of carbapenemase-producing Enterobacteriaceae (CPE) from colonized patients in a Spanish university hospital during a cluster-randomized study [the Resistance of Gram-Negative Organisms: Studying Intervention Strategies (R-GNOSIS) project] on isolation strategies for faecal ESBL carriers. From March 2014 to March 2016, 15556 rectal swabs from 8209 patients admitted in two surgical wards and two medical wards were collected and seeded on ESBL and CPE chromogenic agars. Carbapenemase characterization (PCR and sequencing) was performed, and antibiotic susceptibility (MIC), clonality (PFGE and MLST) and diversity (Simpson diversity index estimation) were determined. One hundred and ninety-eight CPE isolates, mainly Klebsiella pneumoniae (53.5%) and Escherichia coli (19.2%), were identified in 162 patients (2%). Prevalence of CPE carriage remained unchanged over time. Overall, amikacin (9.6%), tigecycline (9.6%) and colistin (0.5%) showed low non-susceptibility. The most frequent carbapenemase was OXA-48 (64.1%), followed by VIM-1 (26.8%), NDM-1 (5.3%) and KPC-3 (3.5%), and these were co-produced with ESBLs in 43.9%. OXA-48 plus CTX-M-15 was the most frequent association. Two major K. pneumoniae clones were identified (OXA-48-CTX-M-15-ST11 and VIM-1-SHV-12-ST54) with considerable genetic diversity among the remaining isolates, including OXA-48-E. coli. Species diversity tended to decrease from 0.75 in the first 6 months of the study to 0.43 in the final months. The emergence of new clones (i.e. OXA-48-Kluyvera spp. and NDM-1-K. pneumoniae ST437 and ST101) and displacement of other particular clones were also demonstrated. We describe a polyclonal and changeable CPE population over time. Coexistence of worldwide disseminated clones, such as ST11-OXA-48- K. pneumoniae, with unrelated and emerging OXA-48-E. coli clones, depicts a disturbing CPE epidemiology in our institution.